Chennai City took a sixth minute lead through Frenchman Jean-Michel Joachim but they were reduced to 10 men after Pradeep Mohanraj was sent off in the 34th minute for handling the ball inside the box.
Ansumana Kromah brought up the equaliser for Mohun Bagan from the resultant penalty in the 36th minute but Chennai City's Veniamin Shumeyko headed home the winner in the 71st minute to script the first big upset of I-League this season.
"I did not have the mentality to continue after this loss and three home draws where we could not come back. We lost at home, I had decided that I would step down if that happened," Sen said at his last press conference at Mohun Bagan tent as unruly crowd hurled missiles at the venue.
Sen was appointed the chief coach for the Mariners in December 2014 after the club parted ways with technical director Subhas Bhowmick and was instrumental in their I- League triumph in the 2014-15.
While United SC became runners-up in IFA Shield and Durand Cup under his tutelage, the Black and Whites won the Shield last season. Sen had also led Mohammedan to become the champions of the I-League second division a couple of seasons back.
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